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- PDB-2lie: NMR structure of the lectin CCL2 -

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Basic information

Entry
Database: PDB / ID: 2lie
TitleNMR structure of the lectin CCL2
ComponentsCCL2 lectin
KeywordsSUGAR BINDING PROTEIN
Function / homology: / CCL2 lectin-like / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / CCL2 lectin
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsSchubert, M. / Walti, M.A. / Egloff, P. / Bleuler-Martinez, S. / Aebi, M. / Allain, F.F.-H. / Kunzler, M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Plasticity of the beta-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System
Authors: Schubert, M. / Bleuler-Martinez, S. / Butschi, A. / Walti, M.A. / Egloff, P. / Stutz, K. / Yan, S. / Wilson, I.B. / Hengartner, M.O. / Aebi, M. / Allain, F.H. / Kunzler, M.
History
DepositionAug 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCL2 lectin


Theoretical massNumber of molelcules
Total (without water)16,6041
Polymers16,6041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein CCL2 lectin


Mass: 16604.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: ccl2 / Production host: Escherichia coli (E. coli) / References: UniProt: B3GA02

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 15N-HSQC
1312D NOESY
1413D 15N edited NOESY
1512D 15N F1-filtered,F2-filtered NOESY
1622D NOESY
1722D TOCSY
1822D 13C-HSQC (at natural abundance)
1922D 15N-HSQC (for H/D exchange)
11032D 13C-HSQC for aliphatic region
11132D 13C-HSQC for aromatic region
11233D 13Cedited-NOESY for aliphatic region
11332D 13Cedited NOESY for aromatic region
11433D HNCA
11533D HN(CA)CB
11633D HNCO
11742D 13C-HSQC for aliphatic region
11842D 13C-HSQC for aromatic region
11943D (H)CCH-COSY
12042D 13C F1-filtered TOCSY
12142D 13C F1-filtered NOESY
12242D 13C F1-filtered, F2-filtered NOESY
12343D 13C F1-edited, F3-filtered NOESY for aliphatic region
12443D 13C F1-edited, F3-filtered NOESY for aromatic region
12552D constant-time 13C-HSQC to unambiguously assign the stereochemical methyl groups of VAL and LEU

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] CCL2, 50 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] CCL2, 50 mM potassium phosphate, 100 mM sodium chloride, 100% D2Osample_2100% D2O
solution31 mM [U-100% 15N] CCL2, 50 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution41 mM [U-100% 15N] CCL2, 50 mM potassium phosphate, 100 mM sodium chloride, 100% D2Osample_4100% D2O
solution51 mM [U-1% 13C; U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, 41 mM [U-100% 2H] acetic acid 95%H2O/5% D2Osample_595% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCCL2[U-100% 13C; U-100% 15N]1
50 mMpotassium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
1 mMCCL2[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
1 mMCCL2[U-100% 15N]3
50 mMpotassium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
1 mMCCL2[U-100% 15N]4
50 mMpotassium phosphatenatural abundance4
100 mMsodium chloridenatural abundance4
1 mMCCL2[U-1% 13C; U-100% 15N]5
1 mMSUGAR (3-MER)natural abundance5
50 mMpotassium phosphatenatural abundance5
100 mMsodium chloridenatural abundance5
41 mMacetic acid[U-100% 2H]5
Sample conditionsIonic strength: 150 / pH: 5.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAHerrmann, Guntert and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR constraintsNOE constraints total: 2514 / NOE intraresidue total count: 482 / NOE long range total count: 1439 / NOE sequential total count: 593 / Hydrogen bond constraints total count: 92 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 95
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å

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